From 178ac5c0832efaed0a89e9334dbfaec7a3cd10ba Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 6 May 2020 12:30:25 -0500
Subject: [PATCH] Fix fastq output name fix
---
workflow/scripts/bdbagFetch.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/workflow/scripts/bdbagFetch.sh b/workflow/scripts/bdbagFetch.sh
index de47b9b..0bf20f0 100644
--- a/workflow/scripts/bdbagFetch.sh
+++ b/workflow/scripts/bdbagFetch.sh
@@ -5,7 +5,7 @@ then
bdbag --resolve-fetch all --fetch-filter filename\$*fastq.gz ${1}
for i in $(find */ -name "*R*.fastq.gz")
do
- path=${2}$.(echo ${i##*/} | grep -o "R[1,2]").fastq.gz
+ path=${2}.$(echo ${i##*/} | grep -o "R[1,2]").fastq.gz
cp ${i} ./${path}
done
elif [ "${3}" == "TEST" ]
--
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